Non-hereditary maximum parsimony trees

DOI10.1007/S00285-011-0458-9zbMATH Open1269.90124arXiv1007.3964OpenAlexW2010275284WikidataQ42613000 ScholiaQ42613000MaRDI QIDQ455749FDOQ455749

Authors: Mareike Fischer 

Publication date: 22 October 2012

Published in: Journal of Mathematical Biology (Search for Journal in Brave)

Abstract: In this paper, we investigate a conjecture by von Haeseler concerning the Maximum Parsimony method for phylogenetic estimation, which was published by the Newton Institute in Cambridge on a list of open phylogenetic problems in 2007. This conjecture deals with the question whether Maximum Parsimony trees are hereditary. The conjecture suggests that a Maximum Parsimony tree for a particular (DNA) alignment necessarily has subtrees of all possible sizes which are most parsimonious for the corresponding subalignments. We answer the conjecture affirmatively for binary alignments on five taxa but also show how to construct examples for which Maximum Parsimony trees are not hereditary. Apart from showing that a most parsimonious tree cannot generally be reduced to a most parsimonious tree on fewer taxa, we also show that compatible most parsimonious quartets do not have to provide a most parsimonious supertree. Last, we show that our results can be generalized to Maximum Likelihood for certain nucleotide substitution models.

Full work available at URL: https://arxiv.org/abs/1007.3964

Recommendations

• Links between maximum likelihood and maximum parsimony under a simple model of site substitution
• Two further links between MP and ML under the Poisson model.
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zbMATH Keywords

maximum likelihoodphylogeneticsmaximum parsimonyJukes-Cantor model

Mathematics Subject Classification ID

Programming involving graphs or networks (90C35) Chemistry (92E99) Applications of graph theory to circuits and networks (94C15)

Cites Work

• Reconstructing the shape of a tree from observed dissimilarity data
• The Steiner problem in phylogeny is NP-complete
• Links between maximum likelihood and maximum parsimony under a simple model of site substitution

Cited In (4)

• On the number of binary characters needed to recover a phylogeny using maximum parsimony
• Two further links between MP and ML under the Poisson model.
• Nonadmissible genealogical trees
• Statistical inconsistency of maximum parsimony for \(k\)-tuple-site data

Uses Software

• PHYLIP

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